dataverse 10.18130 V3 F3TD5R d4d

Datasheet for Dataset - Human Readable Format

🎯

Motivation

Why was the dataset created?

  • Name
    Intended Purpose
    Response
    AI-ready datasets to support research in functional genomics
GrantorGrant NameGrant Number
National Institutes of Health1OT2OD032742-011OT2OD032742-01
📊

Composition

What do the instances represent?

  1. Name
    Data Modalities and Instances
    Representation
    Multimodal cellular measurements from human cell lines (iPSCs and disease-relevant lines)
    Instance Type
    Perturb-seq (scRNA-seq), SEC-MS protein-protein interaction profiling, immunofluorescence (IF) images
    Data Type
    Mixture of raw data (images, sequencing reads hosted externally) and processed data/metadata packaged via RO-Crate and Dataverse artifacts
    Sampling Strategies
    1. Name
      Sampling and Representativeness
      Is Sample
      • True
      Is Random
      • False
      Source Data
      • Commercially available de-identified human cell lines (e.g., KOLF2.1J iPSCs; MDA-MB-468)
      Is Representative
      • False
      Why Not Representative
      • Does not represent all biological variants seen in the wider population
      Strategies
      • Targeted selection of proteins and perturbations across specified cell types and treatments
    Missing Information
    • Name
      Known Omissions
      Missing
      • Computed cell maps not included in this release
      Why Missing
      • To be added in future releases
  • Name
    Cell Types and Conditions
    Identification
    • Undifferentiated KOLF2.1J iPSCs
    • iPSC-derived NPCs
    • iPSC-derived neurons
    • iPSC-derived cardiomyocytes
    • MDA-MB-468 breast cancer cells (treated and untreated)
    Distribution
    • Overlapping but non-identical protein sets across SEC-MS, IF, and perturb-seq modalities
  • Name
    Distribution Channels and Formats
    Description
    • Dataverse package with RO-Crate metadata, HTML datasheet, provenance graphs, and ZIP archives of images
    • External repositories for raw modality data (SRA, MassIVE)
DescriptionName
2025-07-01Initial Release
2025-10-22Additional Image Archives
  • Description
    The dataset is hosted publicly on Dataverse; some subsets may be under temporary embargo.
🔍

Collection Process

How was the data acquired?

doi:10.18130/V3/F3TD5R
Cell Maps for Artificial Intelligence - June 2025 Data Release (Beta)
Cell Maps for Artificial Intelligence - June 2025 Data Release (Beta)
This dataset is the June 2025 Data Release of Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org), the Functional Genomics Grand Challenge in the NIH Bridge2AI program. This Beta release includes perturb-seq data in undifferentiated KOLF2.1J iPSCs; SEC-MS data in undifferentiated KOLF2.1J iPSCs, iPSC-derived NPCs, neurons, cardiomyocytes, and treated and untreated MDA-MB-468 breast cancer cells; and IF images in MDA-MB-468 breast cancer cells in the presence and absence of chemotherapy (vorinostat and paclitaxel).
https://doi.org/10.18130/V3/F3TD5R
2025-07-01
2025-02-27
  • AI
  • artificial intelligence
  • machine learning
  • Bridge2AI
  • CM4AI
  • induced pluripotent stem cell
  • iPSC
  • KOLF2.1J
  • neural progenitor cell
  • NPC
  • neuron
  • cardiomyocyte
  • breast cancer
  • MDA-MB-468
  • paclitaxel
  • vorinostat
  • perturb-seq
  • perturbation sequencing
  • single-cell RNA sequencing
  • scRNAseq
  • SEC-MS
  • size exclusion chromatography
  • protein-protein interaction
  • affinity purification
  • AP-MS
  • mass spectroscopy
  • protein localization
  • subcellular imaging
  • Clark T (University of Virginia)
  • Parker J (University of California, San Diego)
  • Al Manir S (University of Virginia)
  • Axelsson U (KTH Royal Institute of Technology)
  • Ballllosero Navarro F (Stanford University)
  • Chinn B (University of California San Diego)
  • Churas CP (University of California San Diego)
  • Dailamy A (University of California, San Diego)
  • Doctor Y (University of California, San Diego)
  • Fall J (KTH - Royal Institute of Technology)
  • Forget A (University of California San Francisco)
  • Gao J (University of California San Diego)
  • Hansen JN (Stanford University)
  • Hu M (University of California San Diego)
  • Johannesson A (KTH - Royal Institute of Technology)
  • Khaliq H (University of California San Diego)
  • Lee YH (University of California San Diego)
  • Lenkiewicz J (University of California San Diego)
  • Levinson MA (University of Virginia)
  • Marquez C (University of California San Diego)
  • Metallo C (University of California San Diego)
  • Muralidharan M (University of California San Francisco)
  • Nourreddine S (University of California San Diego)
  • Niestroy J (University of Virginia)
  • Obernier K (University of California San Francisco)
  • Pan E (University of California San Diego)
  • Polacco B (University of California San Francisco)
  • Pratt D (University of California San Diego)
  • Qian G (University of California San Diego)
  • Schaffer L (University of California San Diego)
  • Sigaeva A (KTH Royal Institute of Technology)
  • Thaker S (University of Alabama at Birmingham)
  • Zhang Y (University of California San Diego)
  • Bélisle-Pipon JC (Simon Fraser University)
  • Brandt C (Yale University)
  • Chen JY (The University of Alabama at Birmingham)
  • Ding Y (University of Texas at Austin)
  • Fodeh S (Yale University)
  • Krogan N (University of California San Francisco)
  • Lundberg E (Stanford University)
  • Mali P (University of California San Diego)
  • Payne-Foster P (University of Alabama)
  • Ratcliffe S (University of Virginia)
  • Ravitsky V (University of Montreal)
  • Sali A (University of California San Diego)
  • Schulz W (Yale University)
  • Ideker T (University of California San Diego)
  • Name
    Gap Addressed
    Response
    Provide interoperable, AI-ready multimodal cellular data across perturb-seq, SEC-MS, and IF imaging modalities
  1. Name
    External Data Links
    External Resources
    • Sequence Read Archive (sra) Data
      NCBI BioProject
    • Mass Spectrometry Data (human Ipscs)
      MassIVE Repository
    • Mass Spectrometry Data (human Cancer Cells)
      MassIVE Repository
    Archival
    • Long-term preservation at University of Virginia Dataverse; external repositories host raw modality data
    Restrictions
    • Some datasets under temporary pre-publication embargo
Name
De-identification
Description
  • Human Subjects
    False
  • De Identified Samples
    True
  • Fda Regulated
    False
  • Name
    Confidentiality
    Description
    • No PII; de-identified human cell line data
  • Name
    Sensitivity
    Description
    • Biomedical laboratory data; not suitable for clinical decision-making without appropriate oversight
  1. Name
    Data Acquisition
    Description
    • High-throughput laboratory measurements including single-cell RNA sequencing (perturb-seq), size exclusion chromatography mass spectrometry (SEC-MS), and immunofluorescence imaging
    Was Directly Observed
    True
    Was Reported By Subjects
    False
    Was Inferred Derived
    Some processed outputs; primary raw measurements acquired directly
    Was Validated Verified
    Not specified in this record
  • Name
    Collection Mechanisms
    Description
    • Laboratory apparatuses and protocols (sequencing instruments for perturb-seq, mass spectrometers for SEC-MS, confocal microscopy for IF); provenance graphs included for some subsets
  • Name
    Contributing Institutions
    Description
    • University of California San Diego; University of California San Francisco; Stanford University; University of Virginia; KTH Royal Institute of Technology; University of Alabama at Birmingham; Yale University; Simon Fraser University; University of Montreal; University of Texas at Austin
  • Name
    Timeframe
    Description
    • Data Creation Date
      2025-02-27; Release publication date: 2025-07-01; Content current as of 2025-06-30; additional image archives published 2025-10-22
  • Name
    Ethical Review and Governance
    Description
    • Data Governance Committee
      Jillian Parker (jillianparker@health.ucsd.edu)
    • Ethical Review
      Vardit Ravitsky (ravitskyv@thehastingscenter.org) and Jean-Christophe Belisle-Pipon (jean-christophe_belisle-pipon@sfu.ca)
  • Name
    Packaging/Metadata
    Description
    • Release provided with RO-Crate metadata and provenance graphs to support reproducibility and reuse
  • Name
    Raw Data Availability
    Description
    • Raw Or Primary Modality Data Accessible Via External Repositories
      SRA BioProject (sequencing) and MassIVE (mass spectrometry)
DescriptionName
Long term preservation in the University of Virginia Dataverse, supported by committed institutional fundsUniversity of Virginia Dataverse
Use Dataverse contact; Project Lead listed as Trey Ideker (UC San Diego)Point of Contact
CompressionDescriptionFormatIDIssuedMd5Media TypeNamePath
HTML datasheet summarizing key release information.release-ro-crate-datasheet.html2025-07-01599c9ece9b88b3ce797b82463b4a1eb4text/htmlrelease-ro-crate-datasheet.htmlrelease-ro-crate-datasheet.html
Release RO-Crate with pointers to sub ro-crates.JSONrelease-ro-crate-metadata.json2025-07-0199f9e00053bff3020fd9832a3a518bbbapplication/jsonrelease-ro-crate-metadata.jsonrelease-ro-crate-metadata.json
ZIPThis dataset displays the spatial localization of 464 proteins of interest in MDA-MB-468 cells treat...cm4ai-ifimages-mda-mb-468-paclitaxel.zip2025-10-220d972b80744344ddeede516a0cf6e3d7application/zipcm4ai-ifimages-mda-mb-468-paclitaxel.zipImages/cm4ai-ifimages-mda-mb-468-paclitaxel.zip
ZIPSpatial localization of 464 proteins in untreated MDA-MB-468 cells, imaged by ICC-IF and confocal mi...cm4ai-ifimages-mda-mb-468-untreated.zip2025-10-22a98affcc05429650c6bb3906cd836d55application/zipcm4ai-ifimages-mda-mb-468-untreated.zipImages/cm4ai-ifimages-mda-mb-468-untreated.zip
ZIPSpatial localization of 464 proteins in MDA-MB-468 cells treated with vorinostat, imaged by ICC-IF a...cm4ai-ifimages-mda-mb-468-vorinostat.zip2025-10-22ad4e68ccc14b0f3349dad3321e7b81b2application/zipcm4ai-ifimages-mda-mb-468-vorinostat.zipImages/cm4ai-ifimages-mda-mb-468-vorinostat.zip
Provenance graph for paclitaxel-treated image subset (download to view).Images-paclitaxel-provenance-graph.html2025-07-01e38e63e4c8dfc5808a5ffa2d7829fc38text/htmlImages-paclitaxel-provenance-graph.htmlImages/paclitaxel/Images-paclitaxel-provenance-graph.html
Provenance graph for untreated image subset (download to view).Images-untreated-provenance-graph.html2025-07-011a3b510f74d3f8647e07c6559ce64ee8text/htmlImages-untreated-provenance-graph.htmlImages/untreated/Images-untreated-provenance-graph.html
Provenance graph for vorinostat-treated image subset (download to view).Images-vorinostat-provenance-graph.html2025-07-0158935fe4e254b31d33fed019f24c7668text/htmlImages-vorinostat-provenance-graph.htmlImages/vorinostat/Images-vorinostat-provenance-graph.html
Provenance graph for mass spectrometry data (cancer cells) (download to view).mass-spec-cancer-cells-provenance-graph.html2025-07-01931ad9b552562024cb84ebe62d1f1838text/htmlmass-spec-cancer-cells-provenance-graph.htmlmass-spec/cancer-cells/mass-spec-cancer-cells-provenance-graph.html
RO-Crate metadata for mass spectrometry (cancer cells).JSONmass-spec-cancer-cells-ro-crate-metadata.json3a7063bb391ea5e05a32ba5da5f4b2f8application/jsonmass-spec-cancer-cells-ro-crate-metadata.jsonmass-spec/cancer-cells/mass-spec-cancer-cells-ro-crate-metadata.json
  • Name
    Usage Warning
    Warnings
    • Large files; Dataverse may require selective downloads or Data Access API for programmatic access
Name
Regulatory Restrictions
Description
  • None specified in this record
no
🚀

Uses

What (other) tasks could the dataset be used for?

NameResponse
Primary TaskAI model training on functional genomics data
Secondary TaskCellular process analysis and mapping of cell architecture under disease, treatment, or genetic pert...
  • Name
    Related Publications
    Description
    • Clark T Et Al. Cell Maps For Artificial Intelligence
      AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. 2024. doi: http://doi.org/10.1101/2024.05.21.589311
    • Nourreddine S Et Al. A Perturbation Cell Atlas Of Human Induced Pluripotent Stem Cells. Biorxiv. 2024. DOI
      https://doi.org/10.1101/2024.11.03.621734
  • Name
    Additional Potential Tasks
    Description
    • Cellular process analysis
    • Analysis of cell architectural changes and interactions under disease processes, treatment conditions, or genetic perturbations
  • Name
    Limitations and Biases
    Description
    • Interim release; computed cell maps not yet included
    • Protein sets interrogated by different modalities incompletely overlap
    • Data derived from commercially available de-identified human cell lines; does not represent all biological variants
  • Name
    Prohibited Uses
    Description
    • Not to be used in clinical decision-making or any context involving patient care without appropriate regulatory oversight and approval
Name
License
Description
  • CC BY-NC-SA 4.0
  • Community norms expect proper citation of the dataset
  • Name
    Dataset Landing Page
    Description
    • University of Virginia Dataverse (see DOI landing page for access and file selection)
📤

Distribution

How will the dataset be distributed?

doi:10.18130/V3/F3TD5R
CC BY-NC-SA 4.0
🔄

Maintenance

How will the dataset be maintained?

2025-10-22
2.0
Name
Maintenance Plan
Description
  • Dataset will be regularly updated and augmented through the end of the project in November 2026
  • Updates on a quarterly basis
Generated on 2025-11-09 10:17:34 using Bridge2AI Data Sheets Schema